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Import New Samples

ICA Cohorts can pull any molecular data available in an ICA Project, as well as additional sample- and subject-level metadata information such as demographics, biometrics, sequencing technology, phenotypes, and diseases.
To import a new data set, select Import files from the left navigation tab underneath Cohorts.
Confirm that the project shown is the ICA Project that contains the molecular data you would like to add to ICA Cohorts.
Choose a data type among
  • Germline
  • Somatic
Choose a study name among existing studies, or create a new study. Studies are used to help sub-divide and structure any project data further, where needed.
Once done, click on Next to proceed to selecting molecular data files, either in VCF.gz or Nirvana JSON.gz format, from our ICA Project's data folder.
The sample identifiers used in the VCF columns need to match the sample identifiers used in subject/sample metadata files; accordingly, if you are starting from JSON files containing variant- and gene-level annotations provide by ILMN Nirvana, the samples listed in the header need to match the metadata files.

Metadata and File Types

Field
Description
Project name
The ICA project for your cohort analysis (cannot be changed.)
Study name
Create or select a study. Each study represents a subset of data within the project.
Description
Short description of the data set (optional).
Job type
Append: Appends values to any existing values. If a field supports only a single value, the value is replaced.
Replace: Overwrites existing values with the values in the uploaded file.
Delete: Deletes the subject and all samples associated with the subject ID.
Subject metadata files
Subject metadata file(s) in tab-delimited format. For Append and Replace job types, the following fields are required and cannot be changed: - Sample identifier - Sample display name - Subject identifier - Subject display name - Sex
Kinship file
Family relationship metadata file(s) in TSV format.
Note: If annotating large sets of samples with molecular data, expect the annotation process to take over 20 minutes per whole genome sample. You will receive an email both when your ingestion begins and when it is complete.